The growing human population and the development of urban areas have led to fragmentation and destruction of many natural habitats but have also created new urban habitats. These environmental changes have had a negative impact on many species of plants and animals, including parasite communities. The aim of present study was to compare the helminth communities of Apodemus flavicollis and Apodemus agrarius in natural and urban habitats. Helminth burdens were assessed in 124 mice, 48 A. flavicollis, and 76 A. agrarius from two managed forests close to the city boundaries and two city parks within Warsaw, Central Poland. In total, eight species of helminths, Nematoda (n = 3), Digenea (n = 2), and Cestoda (n = 3), were identified. Helminth community structure and prevalence/abundance of individual helminth species differed significantly between the two Apodemus species. Overall, prevalence and abundance of helminth species were significantly higher in A. agrarius compared to A. flavicollis. For A. flavicollis, higher prevalence and abundance of helminths were detected in individuals from managed forest habitats in comparison to city parks. In striped field mice, much higher prevalence and mean abundance were recorded in rodents trapped in city parks than in managed forests. This phenomenon may be explained by better adaptation of A. agrarius, compared to A. flavicollis, to city habitats, resulting in high local densities of mice and the full range of parasite species affecting this host species. Our data confirm also that the established routes of infection exist for selected helminth species in the urban environment.